[Bioc-devel] Omada package failing due to removed dependency

Sokratis Kariotis @okr@t|@k@r|ot|@ @end|ng |rom gm@||@com
Mon Jul 31 13:16:08 CEST 2023 

Hey all,

I created a new key and now I can commit etc but there is a conflict that
is not allowing me to go ahead.

My commands:
git add .
git commit -m "Update metrics"
git push upstream main:devel

*The above results in the following error:*













*Enumerating objects: 19, done.Counting objects: 100% (17/17), done.Delta
compression using up to 16 threadsCompressing objects: 100% (11/11),
done.Writing objects: 100% (11/11), 4.78 KiB | 4.78 MiB/s, done.Total 11
(delta 7), reused 0 (delta 0), pack-reused 0remote: Error: You cannot push
without resolving merge conflicts.remote:remote: Please check the files in
the commit pushed to the git-serverremote: for merge conflict markers like
'<<<<<<<', '========', '>>>>>>>'.remote:To
git.bioconductor.org:packages/omada ! [remote rejected] main -> devel
(pre-receive hook declined)error: failed to push some refs to
'git.bioconductor.org:packages/omada'*



On Mon, Jul 31, 2023 at 3:36 PM Mike Smith <grimbough using gmail.com> wrote:

> Hi Sokratis,
>
> Everything in Bioconductor is built around the central Bioconductor git
> repositories.  The only way to get changes out to users is to commit them
> to git.bioconductor.org and then the build system will pick those up, run
> the tests and checks, create new versions of packages, and make them
> available for distribution.
>
> Perhaps you can include the git command you're running to submit the
> changes and a copy of the exact error you're receiving.  That might help
> the team suggest a solution.
>
> Best regards,
> Mike
>
> On Fri, 28 Jul 2023 at 08:32, Sokratis Kariotis <
> sokratiskariotis using gmail.com> wrote:
>
>> Hey both,
>>
>> I have edited the package code but I'm having some difficulties pushing it
>> to trigger another build (github passphrase). Is there another way to
>> trigger the build? Thanks!
>>
>> Cheers,
>> Sokratis
>>
>> On Wed, Jul 12, 2023 at 1:43 AM Kern, Lori <Lori.Shepherd using roswellpark.org
>> >
>> wrote:
>>
>> > We can give you a little more time (a few weeks) to fix the package but
>> > please fix as soon as possible to avoid deprecation.
>> >
>> > Cheers,
>> >
>> > Lori Shepherd - Kern
>> >
>> > Bioconductor Core Team
>> >
>> > Roswell Park Comprehensive Cancer Center
>> >
>> > Department of Biostatistics & Bioinformatics
>> >
>> > Elm & Carlton Streets
>> >
>> > Buffalo, New York 14263
>> > ------------------------------
>> > *From:* Sokratis Kariotis <sokratiskariotis using gmail.com>
>> > *Sent:* Monday, July 10, 2023 10:27 AM
>> > *To:* Kern, Lori <Lori.Shepherd using RoswellPark.org>
>> > *Cc:* Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com>;
>> > bioc-devel using r-project.org <bioc-devel using r-project.org>
>> > *Subject:* Re: [Bioc-devel] Omada package failing due to removed
>> > dependency
>> >
>> > Hey both,
>> >
>> > I have checked the package license (GPL) and it should be fine to use
>> the
>> > code. However, I am having difficulty finding the actual code to
>> calculate
>> > the internal metrics I am using (used in Omada's function
>> > cluster_voting.R). I can only find the wrapper function but not the ones
>> > that actually calculate the metrics. I am not sure how to proceed with
>> this
>> > in time, so the Omada package won't get deprecated.
>> >
>> > Regards,
>> > Sokratis
>> >
>> > On Fri, Jul 7, 2023 at 1:03 AM Kern, Lori <
>> Lori.Shepherd using roswellpark.org>
>> > wrote:
>> >
>> > We would not hunt down the lab especially for CRAN packages,  but you
>> > could reach out if you like.  That would probably be a recommended
>> action
>> > to either ask someone from their lab to maintain or if you are willing
>> and
>> > you really want the package around you could ask the lab if they mind
>> you
>> > volunteering to be the new maintainer.
>> >
>> > There could see two options for rewriting/maintaining.
>> >
>> > 1. Take over maintenance of the package and resubmit to CRAN
>> > It's a little tricky cause this is a CRAN package so I'm not sure on
>> their
>> > exact policy of taking over an abandoned package. If this is desired,  I
>> > would reach out to CRAN to find out their exact policy
>> > 2. Move needed code to your Bioconductor package
>> > You'll have to check the original package license to make sure this is
>> > allowed under the license of the package. You will still want to give
>> the
>> > original authors/maintainer credit. I would say to be safe I would
>> include
>> > them as contributors/authors in the DESCRITPION Authors using R field and in
>> > the R code I would add a comment above the code to reference original
>> > package citation and stating it was copied from there.  I'm not a
>> lawyer or
>> > license/copy right expert so not sure if that would be good enough but
>> that
>> > would be my take on it.
>> >
>> > Lori Shepherd - Kern
>> >
>> > Bioconductor Core Team
>> >
>> > Roswell Park Comprehensive Cancer Center
>> >
>> > Department of Biostatistics & Bioinformatics
>> >
>> > Elm & Carlton Streets
>> >
>> > Buffalo, New York 14263
>> > ------------------------------
>> > *From:* Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com>
>> > *Sent:* Thursday, July 6, 2023 1:58 AM
>> > *To:* Sokratis Kariotis <sokratiskariotis using gmail.com>
>> > *Cc:* Kern, Lori <Lori.Shepherd using RoswellPark.org>;
>> bioc-devel using r-project.org
>> > <bioc-devel using r-project.org>
>> > *Subject:* Re: [Bioc-devel] Omada package failing due to removed
>> > dependency
>> >
>> > https://nonstationarity.sciencesconf.org/resource/page/id/7
>> > <
>> https://secure-web.cisco.com/1pCvxIL3lfzw2yMAoq1pXQ5JiavYeyZHI2qtDauHw4xwZZBxaV-dAKGWcVKgwz09vF4YJJGVvkcQloDj0mJOUxj7BI3WPu_1Ze3vDW0a9syxuRsiQNOGsRkJ8BaWBdlxOdRBAw39KujDDGqb_DPfL6IsjHK5UCqoCpzw39GduVcBLFIutoPM8Nqjgp8ArDuh-oK-Bxe-huDYCoLXUX5GyU_fEG81AEtF-osCFtJNLRiQBggrsxcViF8mNihzVj8-UT4cNawHmz7xye_KNs45WZOxnVljiq5QQHuIGCeXRkbYBUvrpcEoTootlVxLloYK0/https%3A%2F%2Fnonstationarity.sciencesconf.org%2Fresource%2Fpage%2Fid%2F7
>> >
>> > That is, perhaps, not surprising...
>> >
>> > Package seems to be too good to be abandoned. I wonder if anyone from
>> > their lab
>> > <
>> https://secure-web.cisco.com/1IisY82Mh0-7_0tTgq7v7MgjvGFKIBucg15oqE_SNpUPzwuvYYaCPgz427Efo9Xga7j3PYM6msIsM8GJAK7ofsjmhrfAG3_kBGCmTdF0gVYBUz17CdZjNygLUpDMXPSt6h5CfKAjX_SrymhwTWvvEuyH1cH3nCYhVkVd5xfdd2W5azA0g9MJ4bPASnxJwY9quFxu_6CAIuYXkkO_DqiO9NC6Nb22USMev1V4qh5A3IX2kg6l60sRbM9gDQWjNwbJAPSnWq9G5setIw9CNP8avnjON5nhm_cjNhhn6s6kY07wwiSQ4sSQqsekskzOjhbm1/https%3A%2F%2Fmodalx.parisnanterre.fr%2Fmembres
>> >
>> > could take over maintenance, if you still bother to ask...
>> >
>> > Best,
>> > Oleksii
>> >
>> > On Thu, 6 Jul 2023 at 06:23, Sokratis Kariotis <
>> sokratiskariotis using gmail.com>
>> > wrote:
>> >
>> > Hey,
>> >
>> > I haven't received any responses from the maintainer of ClusterCrit so I
>> > guess I will have to re-write the code used. How can I properly go about
>> > this and credit the authors as well? Thanks!
>> >
>> > Cheers,
>> > Sokratis
>> >
>> > On Thu, Jun 29, 2023 at 7:38 PM Kern, Lori <
>> Lori.Shepherd using roswellpark.org>
>> > wrote:
>> >
>> > We do not allow archived packages to be used.  All dependencies must be
>> on
>> > CRAN or Bioconductor. So yes if you can get them to reinstate the
>> package
>> > on CRAN that would be ideal.  If not you will have to remove the package
>> > from the dependency list and either re-write the code used (giving
>> original
>> > clusterCrit authors credit) or remove the functionality used from that
>> > package.
>> >
>> > Lori Shepherd - Kern
>> >
>> > Bioconductor Core Team
>> >
>> > Roswell Park Comprehensive Cancer Center
>> >
>> > Department of Biostatistics & Bioinformatics
>> >
>> > Elm & Carlton Streets
>> >
>> > Buffalo, New York 14263
>> > ------------------------------
>> > *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
>> > Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com>
>> > *Sent:* Thursday, June 29, 2023 5:36 AM
>> > *To:* Sokratis Kariotis <sokratiskariotis using gmail.com>
>> > *Cc:* bioc-devel using r-project.org <bioc-devel using r-project.org>
>> > *Subject:* Re: [Bioc-devel] Omada package failing due to removed
>> > dependency
>> >
>> > Hi,
>> > in this case maybe it's worth reaching out to the maintainer of
>> > clusterCrit. It was removed from CRAN because of (seems-to-be) minor
>> > warnings, which can be addressed by the clusterCrit developer in no
>> time...
>> >
>> > Best,
>> > Oleksii
>> >
>> > On Thu, 29 Jun 2023 at 08:44, Sokratis Kariotis <
>> > sokratiskariotis using gmail.com>
>> > wrote:
>> >
>> > > Dear Bioconductor team,
>> > >
>> > > I received an email that my package "Omada" is failing in release and
>> > > devel. I had a look and the problem seems to be: *ERROR: dependency
>> > > ‘clusterCrit’ is not available for package ‘omada’*. So the package
>> > > clusterCrit was removed. Is there a way I can use a archived version
>> of
>> > it
>> > > (or something similar) so I don't have to rewrite code based on new
>> > > packages to avoid potentially inconsistencies? Please advise, thank
>> you!
>> > >
>> > > Cheers,
>> > > Dr. Sokratis Kariotis (PhD)
>> > > Agency for Science, Technology and Research (A*STAR)
>> > > Singapore Immunology Network (SIgN)
>> > > Twitter: @s_kariotis <
>> >
>> https://secure-web.cisco.com/1EqWv8V2N5hRbw3HmoPEY8RdpEeWxqDoUa71DV8jQUiygXZiRjRxTOSFFWWDUSN7nw3Aviue7E_1xQuvbY4J8O3un4nvR0wtrlQUjMbs1vFGt5o9bI_InwlMvRWb2dhIe9ic0_2ugbdCwXwW_RGN1G4LJxUxm_yO9EkGSnc10bfG2fjit4oALm7Y8gMqnFusMJfqR3j-IKbu0Hem-jPRYXIeAurGmn1l7FvPYk9Pi6MHnOl1RN-5x19R655qOhP8vtsh9q-qwvckAbwuklQvq6lo0zKstGTdB6JkFCIIHswJrur4WrdjGMtwrYkWwOAQs/https%3A%2F%2Ftwitter.com%2Fs_kariotis
>> > >
>> > > LinkedIn:
>> >
>> http://secure-web.cisco.com/1hrH0VDgCpCKm6BWl_eP9v57iZE2j6Y9RUetJ4RMrKylsFeYV7AWyeBfOewj6SpLxhrD-_JnI4sPdaUJB9Mwxuj-B5ot2FZIu4AU87ty04CdxW8zw9DShqtsaZPm68os9ySeI12kEcN_iujEcY11StQo1_qKeBsQchHO3Vc_qvfAbA2T29jSt4KX0OnG4UZENEfns3cigBqNgiYMOOiCGmz01_nIY5M3cgVbsTmSNA-pov7ZD6si4bOXF6pt-manBCeK0NB13icO5MMlpc8HNxSqkARD7n-R71Sa3ZsGQOIYPgA0uuuIRAR9DbV_F5kSj/http%3A%2F%2Fwww.linkedin.com%2Fin%2Fsokratiskariotis
>> > >
>> > >         [[alternative HTML version deleted]]
>> > >
>> > > _______________________________________________
>> > > Bioc-devel using r-project.org mailing list
>> > >
>> >
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>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel using r-project.org mailing list
>> >
>> >
>> https://secure-web.cisco.com/1CoMZlPPSNe-MfqZkOpNFvpMkwbnIVkEbPIxbET9FKoHMGCVzTeeTdPJGpD4PHivCSzZwalSMt8BeA1_Ab8Pa5gS2jCkg9_onfbYE3UAgbywg5GD1CrAN86qgN8FH4tjTwPBq95yDFIvYCamr14TUrSDkZKUvFhtAw7FR6bpJ_Ub9z2fU6f-G3Xw_FHRqcg6aM9xrpq4GmnfMOKO_Jlf10TJsdvhdReM9Phw2lV_EMy55ZjFYD5bteCpN4_qqRQb4_J6IbFYjlRQEi1A0DiwxC67Gzaf0QPTRszxXRxqPy4oancisQKzNmQJod-2cz9Oa/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>> >
>> >
>> > This email message may contain legally privileged and/or confidential
>> > information. If you are not the intended recipient(s), or the employee
>> or
>> > agent responsible for the delivery of this message to the intended
>> > recipient(s), you are hereby notified that any disclosure, copying,
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>> > received this message in error, please notify the sender immediately by
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>> >
>> >
>> >
>> > --
>> > Cheers,
>> > Sokratis Kariotis
>> > PhD Student
>> > University of Sheffield, Medical School
>> > MedTech
>> > <
>> https://secure-web.cisco.com/1j_t_6XlNHmK_Mlrd4WRabc9QOpzT2OGES5vH7ZXf-zkhvpeT6fGj6r1c6HMwcYrnxIzGZ6HwikAhhXIh8OkaEgWqigSPXAd_m0NPSjZf7cr7xi4b003k8sYSFAOfwcStP8WCMJQEHURgiHkNDvUmrUdfJYydQO9lMNOyfaP6SnxI2mQX21fOBWIj5wlIAVh9_pBFujbt_XfCBhHL495EtB_s0ntbiowBalE7bhEa4FullCdFTSex4VfICmSriWx91cSPmk1TzmAHv6KZtr7XqAgLH4OzGlGEUTMdjmcrYOoLTC5XpKAljIZMsCwu8hDP/https%3A%2F%2Fwww.facebook.com%2Fmedtechsheffield%2F
>> >
>> > President
>> > Twitter: @s_kariotis
>> > <
>> https://secure-web.cisco.com/13IN8xWDrADy-iyp1mknOrX5y2tJixhXPBcywL3EoIE7tOUCkSYs7hbAy2slZfzwMH3Bq9AnScXs3HK_KnDOO2kihBQdfM9nIHxnoa1vAkVFfYH8L_ns7w9KGqC0pzUOOxThE_ZMGVWk1LyQyf-RPrv_HY7RqQZo1IEYNirDTKWBu2lkLCH8qvs8lRMm79wx5eRwdZVYNH0uq7g7EcP_vvK9d8vQ534dzt0hOgHaDByQVi2reoXzwifR0pOYP-6LhdI15nbDtZHxMBmTvueysM77gfHBn7_IUHK6y9-biSIidTmH3GlJMkhk83x7UR5Jk/https%3A%2F%2Ftwitter.com%2Fs_kariotis
>> >
>> > LinkedIn: http://www.linkedin.com/in/sokratiskariotis
>> > <
>> http://secure-web.cisco.com/1h1oCsLmDI6MQdDDyPKrhabJrDBtBogVZA8wMdTLiZENtCtnsB9UQqak12XHMegX9sP0mimjSxawrR5u0VlKLv-D4lrX8u8A05PST1zfXM9VJX6E41Hj2-TOTZm9uOWc8hfxBrCT6UPjQ0X5pFh0sQRgC5tqu2Ks1EALVXZvSixGddS_zQ2C0bQhnc9KLJe8J3jtxPOkUz7QqCjcwpfgixL9ls_ysxmn2OGFxfiMwTmWgUXWcfWwvOXy6OhfeAl_IDK9USdONEsQETuVSgt7f2eVi5DJJBy_4eVwIVz3GV6iTGr2VjRBlh98HxZMAr-iP/http%3A%2F%2Fwww.linkedin.com%2Fin%2Fsokratiskariotis
>> >
>> >
>> >
>> > This email message may contain legally privileged and/or confidential
>> > information. If you are not the intended recipient(s), or the employee
>> or
>> > agent responsible for the delivery of this message to the intended
>> > recipient(s), you are hereby notified that any disclosure, copying,
>> > distribution, or use of this email message is prohibited. If you have
>> > received this message in error, please notify the sender immediately by
>> > e-mail and delete this email message from your computer. Thank you.
>> >
>> >
>> >
>> > --
>> > Cheers,
>> > Sokratis Kariotis
>> > PhD Student
>> > University of Sheffield, Medical School
>> > MedTech
>> > <
>> https://secure-web.cisco.com/1EbU56JtxgdwdoJoUZSkRfzViaYzT5UpVv7Wn4bHXpw7_iNUn_et52ACzsUWbzs2Du309DRo4wtQgGcVuDWVIPx5vtUsOovTfb6A-HIBq3NSje0v9lBELQCeYZvBzjm0t2kAdce_aXnf8m3mH7-cYUd0C6Wu2R7erAmQwuoI22clJuDcztgq-JhMyIczKcN_UhCUNAzJ-b_kHKI3mxzoO76dg0N8g2MIp_pHBC3x0rVQno00wElfOCtr3poLLQZwpcZCTPoAQmYs-Dfin4Lwoy2-B9Qn5txtHoCygaeneDxgiTHVOAuILij26i2Q9cgAQ/https%3A%2F%2Fwww.facebook.com%2Fmedtechsheffield%2F
>> >
>> > President
>> > Twitter: @s_kariotis
>> > <
>> https://secure-web.cisco.com/1RhhMUBj_mRXVHCOKQB6We-WITw332tSjBMu7_BVsJxiUs4tE1EO3zyDwMwygB4WIh8AaEo6gPZZcTCl81Qy6PrClu7SxtC3TbzSz30XZlzOjZukAKbowWtBHiJ36lG-a4U_5dYeM6CKUfdb7MaXesg8oLlZscBYO4fVVKMdcjn0NvtsvF-RfOVtu8tVFiOw6yvb3Rt1g-2xPBcrCEEn69L2z59SnUHY8pboO84aP6YBHHPhMHXw1Quz5J7KfGN3qlcX3kehRg0RIISJKLCdu87PnMhtcbODE0T15xmjyc1mUYKmjlmwghgZF4m-UzFoP/https%3A%2F%2Ftwitter.com%2Fs_kariotis
>> >
>> > LinkedIn: http://www.linkedin.com/in/sokratiskariotis
>> > <
>> http://secure-web.cisco.com/1QlRJ-HwDhYoeQZGt2FCzKpzCEleTeJuBprI0G9qystL3HbJH4unSUkFhwBB5vlm1EWz9u50EG4S0Xnv38OXhu3-ioroUBcS0KG6x7V3cFf73lNR3mJnwnqVqzPtq9gIMtUxwnPPzS6sHVbJhDi2CyejXNt0HoO5oRi4T3Ruca3MN7ZxxXJd2gbyGVGryXBDFLrVBlg3KZ-3_m8AFoTvBpUvWv7fs0vGBQ2lWUXSoQ7JYARZ0vy5mW0a4kK2EzbxCWaOFLR6JcbDwA3T9BO006AtSM2onHVqveK_jx2VZB6CvZsLrR-VJ4j41A8IvYfuQ/http%3A%2F%2Fwww.linkedin.com%2Fin%2Fsokratiskariotis
>> >
>> >
>> > This email message may contain legally privileged and/or confidential
>> > information. If you are not the intended recipient(s), or the employee
>> or
>> > agent responsible for the delivery of this message to the intended
>> > recipient(s), you are hereby notified that any disclosure, copying,
>> > distribution, or use of this email message is prohibited. If you have
>> > received this message in error, please notify the sender immediately by
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>> >
>>
>>
>> --
>> Cheers,
>> Sokratis Kariotis
>> PhD Student
>> University of Sheffield, Medical School
>> MedTech <https://www.facebook.com/medtechsheffield/>President
>> Twitter: @s_kariotis <https://twitter.com/s_kariotis>
>> LinkedIn: http://www.linkedin.com/in/sokratiskariotis
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

-- 
Cheers,
Sokratis Kariotis
PhD Student
University of Sheffield, Medical School
MedTech <https://www.facebook.com/medtechsheffield/>President
Twitter: @s_kariotis <https://twitter.com/s_kariotis>
LinkedIn: http://www.linkedin.com/in/sokratiskariotis

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